I have a couple of questions regarding my RNA-Seq experiment but I will start with a hopefully easy one.
I have three batch-effects in my design. Unfortunately, one of these effects contain two batches with only one sample. I found one post here, which recommended not to use such batch-effects (see: here in the next-to-last comment). My question is, is this right and can someone explain why (it makes sense but I can not explain why).
My second question also refers to the batch-topic. Let's assume I can use two of my batch-variables (these are factor-variables with at least 3 samples per batch), how do I define the design for DESeq2?
I read in the same post, referenced above, that one should put the variable of interest to the end of the design-formula like:
~batch1 + batch2 + condition
Again the question, whether this is correct?
Many thanks for your help. If this is clarified I will continue with my other questions.